Publication details

Split Membrane: A New Model to Accelerate All-Atom MD Simulation of Phospholipid Bilayers

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Authors

KHODAM HAZRATI Mehrnoosh SUKENÍK Lukáš VÁCHA Robert

Year of publication 2025
Type Article in Periodical
Magazine / Source Journal of Chemical Information and Modeling
MU Faculty or unit

Central European Institute of Technology

Citation
web https://pubs.acs.org/doi/10.1021/acs.jcim.4c01664
Doi http://dx.doi.org/10.1021/acs.jcim.4c01664
Keywords FORCE-FIELD; CRYSTAL-STRUCTURE; CHARMM; GUI; VALIDATION; AMBER; POTENTIALS; DIFFUSION; EXTENSION; INSERTION
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Description All-atom molecular dynamics simulations are powerful tools for studying cell membranes and their interactions with proteins and other molecules. However, these processes occur on time scales determined by the diffusion rate of phospholipids, which are challenging to achieve in all-atom models. Here, we present a new all-atom model that accelerates lipid diffusion by splitting phospholipid molecules into head and tail groups. The bilayer structure is maintained by using external lateral potentials, which compensate for the lipid split. This split model enhances lateral lipid diffusion more than ten times, allowing faster and cheaper equilibration of large systems with different phospholipid types. The current model has been tested on membranes containing PSM, POPC, POPS, POPE, POPA, and cholesterol. We have also evaluated the interaction of the split model membranes with the Disheveled DEP domain and amphiphilic helix motif of the transcriptional repressor Opi1 as representative of peripheral proteins as well as the dimeric fragment of the epidermal growth factor receptor transmembrane domain and the Human A2A Adenosine of G protein-coupled receptors as representative of transmembrane proteins. The split model can predict the interaction sites of proteins and their preferred phospholipid type. Thus, the model could be used to identify lipid binding sites and equilibrate large membranes at an affordable computational cost.
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